Sequence
atgc intronic sequence ATGC exonic sequencegtttcttttttctgttccttgcaatgaatttgttaagaaattggtggcctttggcatctagaggatagttattgtgaatttcattgtgatacggtgctgatttgaatttactgaatttgccaattatatcttcatctaaaaaaaagttctattttgccagCCTGGTCCGGATTCGGTTGGGATCTTTGCCATTTCACAAAGTTGCAGTGGAGTGGCAGCTCGAGCCTGTGGTCTTGTTAGTTTAGAACCTACGAAG
Basic information
species | Glycine max |
transcript | GLYMA12G08080.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G08080.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g01890.2 (Oryza sativa), 3'ss of exon 5
gtttcttttttctgttccttgcaatgaatttgttaagaaattggtggcctttggcatctagaggatagttattgtgaatttcattgtgatacggtgctgatttgaatttactgaatttgccaattatatcttcatctaaaaaaaagttctattttgccagCCTGGTCCGGATTCGGTTGGGATCTTTGCCATTTCACAAAGTTGCAGTGGAGTGGCAGCTCGAGCCTGTGGTCTTGTTAGTTTAGAACCTACGAAG
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--------------------------------------------------gttccatgctagcactgtttgtttttttgttc--tgtgatttg-tgctaagaggtttttacttgaagtgcttactacccttttgt-----------tttcatgatgtaagCCTGGTCCGGATTCGGTTGGTATTGTGGCCATTTCACATGGTTGCCGTGGTGTTGCTGCCCGTGCCTGTGGTTTGGTGAACCTAGAACCAACAAAA
upper sequence: GLYMA12G08080.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G60690.1 (Arabidopsis thaliana), 3'ss of exon 4
gtttcttttttctgttccttgcaatgaatttgttaagaaattggtggcctttggcatctagaggatagttattgtgaatttcattgtgatac---ggtgctgatttgaatttactgaatttgccaattatatcttcatctaaaaaaaagttctattttgccagCCTGGTCCGGATTCGGTTGGGATCTTTGCCATTTCACAAAGTTGCAGTGGAGTGGCAGCTCGAGCCTGTGGTCTTGTTAGTTTAGAACCTACGAAG
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-------------------------------------------------------------------gttat-acgcatctcgtatcattacttaagtgttatttt--atctgttgatatctatggcaatatgtgaaa-tattgaaatgttgtgtgttgt-agCCTGGTCCGGATTCGGTTGGCATCTTTGCCATTTCGCAAAGATGCAATGGAGTGGCAGCTCGAGCCTGTGGTCTTGTTAGCTTAGAACCTATGAAG
upper sequence: GLYMA12G08080.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv06s0004g02800.t01 (Vitis vinifera), 3'ss of exon 4
gtttcttttttctgttccttgcaatgaatttgttaagaaattggtggcctttggcatctagagg-----atagttattgtgaatttcattgtgatacggtgctgatttgaatttactgaatttgccaattatatcttcatctaaaaaaaagttctattttgccagCCTGGTCCGGATTCGGTTGGGATCTTTGCCATTTCACAAAGTTGCAGTGGAGTGGCAGCTCGAGCCTGTGGTCTTGTTAGTTTAGAACCTACGAAG
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---------------gttttgcattttcttctataaagaattgttttcttcttcattctatatgcttttattgatatagtgtgtttc-tcacaatataatgctgaagcg---tttctgagttgattgttta-attttgttgttga-----------tgctgtcagCCTGGTCCGGATTCGGTTGGGATCTTTGCCATTTCACATAGTTGCAGTGGAGTGGCAGCTCGAGCATGCGGTCTTGTAAGTTTAGAACCCTCAAAGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|24136783|gb|BU927293.1|BU927293EST: CAAAGGCTACAGGAACTGCTGTAGATTGGGTCCAGATGCCTGGGATGAAG CCTGGTCCGGATTCGGTTGGGATCTTTGCCATTTCACAAAGTTGCAGTGGA
genomic: CAAAGGCTACAGGAACTGCTGTAGATTGGGTCCAGATGCCTGGGATGAAGgtttcttttt ... attttgccagCCTGGTCCGGATTCGGTTGGGATCTTTGCCATTTCACAAAGTTGCAGTGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttactgaatttgccaattatatcttcatctaaaaaaaagttctattttgccagCCTGGTCCGGATTCGGTTGGGATCTTTGCCATTTCACAAAGTTGCAGTGGAGTGGCAGCTCGAGCCTGTGGTCTTGTTAGTTTAGAACCTACGAAG
atctaaa putative branch site (score: 3)
ttctatttt putative PPT
aattatatcttcatct TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
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gtttcttttttctgttccttgcaatgaatttgttaagaaattggtggcctttggcatctagaggatagttattgtgaatttcattgtgatacggtgctgatttgaatttactgaatttgccaattatatcttcatctaaaaaaaagttctattttgccagCCTGGTCCGGATTCGGTTGGGATCTTTGCCATTTCACAAAGTTGCAGTGGAGTGGCAGCTCGAGCCTGTGGTCTTGTTAGTTTAGAACCTACGAAG
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